The mission quickly outgrew its first small church and had soon completed a quadrangle and a larger church. Barracks, housing for 1,000 neophytes, workshops and store rooms surrounded the quadrangle. The buildings had tile roofs. The church is rectangular, 185 feet long and 35 feet wide. The walls taper from five feet thick at the base to three feet thick at the top.

The convento (missionary quarters) at San Fernando is unusual. It was added later, and not connected to the main church. Because of the large number of visitors to the mission, the convento was enlarged until it was finally two stories high, 243 feet long and 50 feet wide, with a front colonnade of 20 arches. It was the largest adobe structure in California. The original convento was completed in 1822, and was used by Colonel John C. Fremont when his army invaded California in 1847.

The 1812 earthquake damaged the church, but sturdy repairs were made and the building would have stood for a long time, were it not for vandals who removed the roof tiles, leaving the adobe walls to be destroyed by rains. The church floor was also dug up by people looking for gold.

Restoration began in 1923, but the buildings were irreparably damaged in an earthquake in 1971. Exact replicas were constructed to replace them.